From szeinfel@fox.cce.usp.br Fri Jan 28 06:45:08 1994 Received: from bee08.uspnet.usp.br for szeinfel@fox.cce.usp.br by www.ccl.net (8.6.4/930601.1506) id GAA10776; Fri, 28 Jan 1994 06:21:03 -0500 Received: from fox.cce.usp.br (fox.cce.usp.br [143.107.70.1]) by bee08.uspnet.usp.br (8.6.4/RISC-CCE2.0) id JAA20112 Received: from localhost (szeinfel@localhost) by fox.cce.usp.br (8.6.4/CONVEX120-CCE2.0) id JAA22990 Date: Fri, 28 Jan 1994 09:00:36 -0300 (BST) From: Rafael N Szeinfeld Subject: Re: info perturbation modelling organic molec. To: Alexander Admiraal cc: CHEMISTRY@ccl.net In-Reply-To: <9401271627.AA01733@balaena.bio.vu.nl> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 27 Jan 1994, Alexander Admiraal wrote: > Hello, > > I need information on using perturbuation theory (? I don't know if this is the > correct name) for modelling interactions between organic molecules. > > To be more specific, interaction is between a large organic molecule, which > serves as a kind of model 'enzyme', and a smaller 'substrate'. Most work > that I have done is molecular modeling use force fields, so I need some basic > references/books which can introduce me to the mathematic concepts behind it, > and some example studies. > > If there is interest I will summarize to the list. > > Thanks, Alex > > ---Administrivia: This message is automatically appended by the mail exploder: > CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator > MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net (port 70 or 73) > Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search > > Hi Alex, I'm quite interested in references on MD/MM, something to really introduce someone into the field. I have available QUANTA 3.3 , POLARIS and WHATIF on an IRIS workstation but as I have no basic references I don't yet understand what can I do and how can I do calculations with these programs in order to have reasonable results not just " computer jokes". I saw some calculations in some papers dealing with protein folding (the autor is M. Levitt) but they don't explain the method properly for a begginer. I would like to reproduce some results in order to learn how the hole thing works so If someone who works in the field (or even with the softwares I've mentioned earlier) wants to teach me it would be great. Sincerly yours, Rafael Najmanovich From JeanLuc.Verschelde@rug.ac.be Fri Jan 28 11:45:13 1994 Received: from mserv.rug.ac.be for JeanLuc.Verschelde@rug.ac.be by www.ccl.net (8.6.4/930601.1506) id LAA13821; Fri, 28 Jan 1994 11:30:01 -0500 Received: from allserv.rug.ac.be by mserv.rug.ac.be with SMTP id AB05303 (5.65c/IDA-1.4.4 for ); Fri, 28 Jan 1994 17:28:56 +0100 Received: by allserv.rug.ac.be (5.0/SMI-SVR4) id AA07629; Fri, 28 Jan 94 17:26:27 +0100 Date: Fri, 28 Jan 1994 17:26:27 +0100 (MET) From: Jean-Luc Verschelde Subject: Protein loops and simulated annealing To: OHIO SUPER Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 710 Hi, Is there free software that does MonteCarlo+Simulated annealing to model protein loops? I tried to contact J.Garnier and V.Collura but didn't succeed to find their electronic addresses. I would really appreciate if someone could help me . Jean-Luc =================================================================================== Verschelde Jean-Luc Lab. for Mathematical Physics Lab. for Biochemistry Krijgslaan 286 S9 9000 Ghent Belgium. Tel.:09/264 47 94 Fax:09/264 49 89 Email:Jeanluc.Verschelde@rug.ac.be =================================================================================== From PA13808%UTKVM1.BITNET@phem3.acs.ohio-state.edu Fri Jan 28 12:05:47 1994 Received: from phem3 for PA13808%UTKVM1.BITNET@phem3.acs.ohio-state.edu by www.ccl.net (8.6.4/930601.1506) id LAA13896; Fri, 28 Jan 1994 11:36:22 -0500 From: Received: from UTKVM1.BITNET (PA13808@UTKVM1) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #3557) id <01H87QKUQ88G9AMLXC@phem3.acs.ohio-state.edu>; Fri, 28 Jan 1994 11:36:13 EST Date: 28 Jan 94 11:35 LCL Subject: BITNET mail follows To: CHEMISTRY@ccl.net Message-id: <01H87QKUQ88I9AMLXC@phem3.acs.ohio-state.edu> Content-transfer-encoding: 7BIT Date: Fri, 28 Jan 94 11:17:43 LCL From: PA13808@UTKVM1 Subject: molecular interactions To: alex ======================================================================== refs on books for beginners in this field include. 1.THEORY OF MOLECULAR INTERACTIONS by I. G. Kaplan(Studies in phys and theoretical chemistry vol 42) Elsevier 1986 2. Intermolececular Interactions from diatomics to biopolymers ED B. Pullman Wiley,NY 1977 3. Weak Intermolecular Interactions in Chemistry and Biology, P.Hobza and R. Zahradnik Elsevier, Amsterdam 1980 4. Theoretical Treament of large molecules and their interactions. part 4 of Theoretical Models of Chemical Bonding, ed Z.B. Maksi c Springer Verlag (ISBN 3 540 52253 0 1990 John E. Bloor Univ TENN(PA13808 at UTKVM1.utk.edu) From adit@Kodak.COM Fri Jan 28 13:45:19 1994 Received: from Kodak.COM for adit@Kodak.COM by www.ccl.net (8.6.4/930601.1506) id NAA15172; Fri, 28 Jan 1994 13:41:10 -0500 Received: from bcc9.kodak.com by Kodak.COM (5.61+/2.1-Eastman Kodak) id AA05059; Fri, 28 Jan 94 13:43:18 -0500 Reply-To: adit@Kodak.COM Received: by bcc9.kodak.com (4.1/SMI-4.1) id AA10277; Fri, 28 Jan 94 12:59:41 EST Date: Fri, 28 Jan 94 12:59:41 EST From: adit@Kodak.COM (Adi Treasurywala) Message-Id: <9401281759.AA10277@bcc9.kodak.com> To: chemistry@ccl.net Subject: PA area Computational Club (?) The Chicago area has a very good and well known one, other areas (like Albany even) can boast of a good one. I have "recently" moved into the Phila area and was wondering if there is a computational chemists' club in this area. If yes how may I sign up? if no is there any interest in starting one (purely INDIVIDUAL ie not linked to a company or university). I apologise for using the worldwide bandwith for this local issue. Please reply to me directly if you have answers. Adi M Treasurywala,Sterling Winthrop Inc,1250 South Collegeville Road, PO Box 5000, Collegeville, PA 19426-0900,Voice (215)983-6610 FAX (215)983-5559, INTERNET adit@kodak.com From alex@iqm.unicamp.br Fri Jan 28 13:56:14 1994 Received: from styx.iqm.unicamp.br for alex@iqm.unicamp.br by www.ccl.net (8.6.4/930601.1506) id NAA15223; Fri, 28 Jan 1994 13:44:31 -0500 Received: from localhost (alex@localhost) by styx.iqm.unicamp.br (8.6.4/8.3) id QAA29963; Fri, 28 Jan 1994 16:41:43 -0200 From: Alexandre Araujo de Souza Message-Id: <199401281841.QAA29963@styx.iqm.unicamp.br> Subject: ATOMIC CHARGES: THANKS! To: CHEMISTRY@ccl.net Date: Fri, 28 Jan 1994 16:41:42 -0300 (GMT-3:00) Cc: alex@styx.iqm.unicamp.br X-Mailer: ELM [version 2.4 PL22] Content-Type: text Content-Length: 7022 Hy! Thanks to everybody who send me sugestions about the origin of the diferences in Mulliken net charges in GAUSSIAN 92 and in GAMESS 93! The fundamental thing that make the results diferent is the fact that basis set in GAUSSIAN and in GAMESS are not identical! Below are copies of some sugestions! ---------------------------------------------------- From Louis.Grace@um.cc.umich.edu Wed Jan 26 22:07:10 1994 Received: from um.cc.umich.edu (him3.cc.umich.edu [141.211.144.23]) by styx.iqm.unicamp.br (8.6.4/8.3) with SMTP id WAA06463; Wed, 26 Jan 1994 22:06:58 -0200 From: Louis.Grace@um.cc.umich.edu Date: Wed, 26 Jan 94 18:56:52 EST To: alex@iqm.unicamp.br Message-ID: <30530523@um.cc.umich.edu> X-MTS-Userid: 7K7R Subject: Atomic Charges (GAMESS 93 vs. GAUSSIAN 92)! Status: RO Dear Alexandre, Sorry if this note is too brief or unclear (my car is illegally parked, but I thought I'd check my mail!). As far as I know, whenever one performs any kind of calculation -- energy, charge distribution, etc. -- the calculation must be done on a molecule whose geometry has been optimized WITH THE SAME BASIS SET. Even two GAUSSIAN 92 runs, if they are performed on molecules which were optimized using different basis sets, but are, otherwise the same, will give two different answers. I would think that even differences in the optimization between that of GAMESS and that of GAUSSIAN 92 might affect this, too. I hope this helps. Louis Grace The University of Michigan Ann Arbor, MI 48109 --------------------------------------------------------------- From comp-chem@iqm.unicamp.br Wed Jan 26 22:37:39 1994 Received: from (server@localhost.iqm.unicamp.br [127.0.0.1]) by styx.iqm.unicamp.br (8.6.4/8.3) with SMTP id WAA06568; Wed, 26 Jan 1994 22:37:36 -0200 Date: Wed, 26 Jan 1994 22:37:36 -0200 Message-Id: <199401262246.RAA22979@www.ccl.net> Errors-To: postmaster@iqm.unicamp.br Reply-To: comp-chem@iqm.unicamp.br Originator: comp-chem@iqm.unicamp.br Sender: comp-chem@iqm.unicamp.br Precedence: bulk From: EDGECOMK@QUCDN.QueensU.CA To: Multiple recipients of list Subject: [COMP-CHEM:4972] atomic charges X-Listprocessor-Version: 6.0b -- ListProcessor by Anastasios Kotsikonas X-Comment: Quantum & computational chemistry list from ccl.net Status: RO Re: differences between G92 and GAMESS charges. The first thing to do here is to check to see that the integral accuracy is the same as well as the convergence criteria for the SCF. Other than that perhaps someone with more GAMESS experience (and G92 as well if there is a problem with the accuracy) can help. Take care. Ken Edgecombe -------------------------------------------------------------------- From roberson@hydroxide.chem.utah.edu Thu Jan 27 00:07:24 1994 Received: from CHEMISTRY.CHEM.UTAH.EDU (chemistry.chem.utah.edu [128.110.196.61]) by styx.iqm.unicamp.br (8.6.4/8.3) with SMTP id AAA06864; Thu, 27 Jan 1994 00:07:14 -0200 Received: from hydroxide.chem.utah.edu by CHEMISTRY.CHEM.UTAH.EDU with SMTP; Wed, 26 Jan 1994 19:07:17 -0700 (MST) Received: by hydroxide.chem.utah.edu (AIX 3.2/UCB 5.64/4.03) id AA09947; Wed, 26 Jan 1994 19:07:05 -0700 Date: Wed, 26 Jan 1994 19:07:05 -0700 From: roberson@hydroxide.chem.utah.edu (Mark Roberson) Message-Id: <9401270207.AA09947@hydroxide.chem.utah.edu> To: alex@iqm.unicamp.br Subject: GAMESS Status: RO Sir: Get your GAMESS manual and turn to Section 4-Further Information. A few pages in you will find "Basis Set References," which discusses first the STO-NG class. There, in note 3, you will find that the scale factors used in GAMESS for Na-Cl differ from those proposed by Pople. I suspect that Pople's code uses his values; this may explain the difference you are seeing. Happy crunching, Mark ----------------------------------------------------------------------- From virtual@quantum.larc.nasa.gov Thu Jan 27 11:15:58 1994 Received: from quantum.larc.nasa.gov (quantum.larc.nasa.gov [128.155.22.48]) by styx.iqm.unicamp.br (8.6.4/8.3) with SMTP id LAA10080; Thu, 27 Jan 1994 11:15:48 -0200 Received: by quantum.larc.nasa.gov (1.37.109.8/server2.4) id AA21348; Thu, 27 Jan 1994 08:14:53 -0500 Message-Id: <9401271314.AA21348@quantum.larc.nasa.gov> Date: Thu, 27 Jan 1994 08:14:53 -0500 From: "Don H. Phillips" To: alex@iqm.unicamp.br Subject: Re: Atomic Charges (GAMESS 93 vs. GAUSSIAN 92)! Status: RO >Note that I used the same geometry in both calculations! And, in fact, >the energy was practly the same! But the Mulliken charges... > > Does it represent a bug in GAMESS 93? >From the GAMESS REFS.DOC we see: An excellent review of the relationship between the atomic basis used, and the accuracy with which various molecular properties will be computed is: E.R.Davidson, D.Feller Chem.Rev. 86, 681-696(1986). STO-NG H-Ne Ref. 1 and 2 Na-Ar, Ref. 2 and 3 ** K,Ca,Ga-Kr Ref. 4 Rb,Sr,In-Xe Ref. 5 ... ... .. 3) M.S.Gordon, M.D.Bjorke, F.J.Marsh, M.S.Korth J.Am.Chem.Soc. 100, 2670-2678(1978). ** the valence scale factors for Na-Cl are taken from this paper, rather than the "official" Pople values in Ref. 2. So your Chlorine basis is not identical between the two calculations. This probably explains the difference in you computed for the (mythical) atomic charges. Don l --------------------------------------------------------------- From mike@si.fi.ameslab.gov Thu Jan 27 12:42:04 1994 Received: from si.fi.ameslab.gov (si.fi.ameslab.gov [147.155.30.128]) by styx.iqm.unicamp.br (8.6.4/8.3) with SMTP id MAA11616; Thu, 27 Jan 1994 12:41:54 -0200 Received: by si.fi.ameslab.gov (AIX 3.2/UCB 5.64/4.03) id AA30413; Thu, 27 Jan 1994 08:42:57 -0600 From: mike@si.fi.ameslab.gov (Mike Schmidt) Message-Id: <9401271442.AA30413@si.fi.ameslab.gov> Subject: charges To: alex@iqm.unicamp.br (Alexandre Araujo) Date: Thu, 27 Jan 94 8:42:56 CST X-Mailer: ELM [version 2.4beta PL7] Content-Type: text Content-Length: 180 Status: RO As you can see from REFS.DOC, the basis sets in GAMESS are not always the same as in Gaussian. This is true for STO-NG chlorine, and this no doubt explains the different results. ----------------------------------------------------------- Again, THANK YOU VERY MUCH! --------------------------------- Alexandre Araujo de Souza. Universidade Estadual de Campinas. Campinas,SP - BRAZIL. E-Mail: alex@iqm.unicamp.br ---------------------------------